Hey Airride I was contemplating the same swap into my 66 fastback. However I dont think its worth the hassle. Header clearance between the shock towers is minimal, so changing spark plugs will be a bear. You can the get plenty of power with a 289/302 based motor. But thats just my thought.
I'm not sure about the difference in shock towers, but I know the windsor will fit, it will be pretty tight and getting the right motor mounts is "fun." As far as the plugs go, you'll get used to changing them, I have a 65 with a cleveland squeezed between the shock towers and it takes about 2 hours to do the plugs which is a breeze compared to the 4+ hours it takes to change the plugs in my 03 Lightning.
64.5-66 towers are the same. Installing a 67/68 tower would get you some more room. There's a few 65/66 cars with that modification sporting FE engines, that I know of.......
Stand by to stand by though, it ain't cheap to do that mod.